I have tried all 3 conflict options of auto, override and skip and each one results the same error of "already exists."

In the end, I deleted the 4 episodes I already had, and then ran the same command line without the override option and it completed OK, but it still does not answer the problem, or maybe I did something wrong?

Failed to process [...] because [...] is an exact copy and already exists

This error message means that you're somehow processing the exact same file twice, and this error message is basically a sanity check to make sure you're not doing something strange. It prevents you from accidentally processing the same files over and over again. If you repeatedly run FileBot on the same files, you need to use some sort of logic to call FileBot only of files that haven't been processed with FileBot before.

2.
If you delete the file that should been skipped, either source or destination, then FileBot can't tell that your way of doing things is not ideal, because it'll look as if you're processing the file for the first time.

3.
There is no way to clear memory, because the destination file is the memory. We shouldn't be talking about how we can trick FileBot into letting you do things you probably shouldn't. We should rather have a look at what you are doing, what you are trying to achieve, why you are doing things the way you are doing them, and then maybe find a better solution or approach.

I see many issue with the command you posted, most notably you seem to be organizing for Plex, but completely ignore the plex naming standard in multiple ways (series folder name does not match series name, no season folder, no title in episode, etc).

Maybe you just want to process recently added files? How come you process the same files again in the first place?

I have acquired files in one folder and wanted to copy them to the Plex folder with the naming convention that my usual command line FileBot + Transmission script works with and which Plex is happy with (at least it works for me!)

This time, becuase the folder size was HUGE, I had started to copy the files from Downloaded folder A to Plex folder B by hand and did 4 of them:-

1.
I see. So normally this wouldn't be an issue then, since you can always just use FileBot the first time around. Without copying a few files manually first.

2.
The amc script works better for incremental tasks because it keeps track of what files have or have not been processed yet. If you already have a transmission-post process script, you can actually just use that, so that automated calls and manual calls do exactly the same.

Yes, this is typically the result if you process the same files over and over, for no good reason, abusing limited resources and breaking things for everyone.

Failed to process [...] because [...] is an exact copy and already exists indicates that there's something seriously broken with how you do things, and instead of working anyway, it forces you to fix things and do it right.

What exactly are you doing?

Why are you processing the exact same file into the exact same path more than once?